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The Microbiome File
Old 09-28-2016, 06:42 PM   #1
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The Microbiome File

Lately, the researchers have been suggesting that much of our health is determined by what lives in us and on us.

Hmmm. Where did these things come from and how long have they been with "me". Is "me" really "me", or am "I" just a collection of human DNA (yes), plus a bunch of random stuff that is hitch hiking along for the ride?

It's proven that your microbiome affects your health in various ways. It's proven that a lack of diversity in your gut microbiome is associated with obesity. What are these little buggers doing, and why has it taken "them" so long to even acknowledge that what lives in you is important?

This thread, not that I can or will attempt to control it, just might explore (with the known wisdom of wise regulars here), how aspects of the human microbiome can be leveraged to improve health. Can a gut microbiome predispositioned to obesity be changed? Will there be advances in knowledge such that "bad actors" in the human microbiome will be quelled?

If this initial post has generated an interest in this topic that you have not yet explored, you may consider reading a few of these (kind of) entertaining entries: uBiome Blog - Love your bacteria! (but don't get your biome sequenced...just read the blog entries). CAUTION: You may encounter a Bristol Stool Chart.

What other places are posting things on the topic of the power of what's living in us?
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Old 09-28-2016, 07:02 PM   #2
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I got interested in this when my MIL died from a C-Dif infection. After massive antibiotics for another infection killed her gut bacteria, the C-Dif moved in and killed her. They are now treating this by reintroducing "good" bacteria to the gut via a stool transplant. Unfortunately too late for her.

Fecal Transplantation (Bacteriotherapy) | Johns Hopkins Division of Gastroenterology and Hepatology
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Old 09-28-2016, 07:03 PM   #3
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Wow... so eating probiotics might improve my weight? Cool.
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Old 09-28-2016, 08:02 PM   #4
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There's some research that indicates eating whole grains - not just products like bread made from whole grain flour - but eating the actual whole grains helps maintain healthy gut flora. Possibly because flour is digested higher in the digestive tract but with whole grains some of the nutrition lasts long enough to reach the gut microbes.
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Old 09-28-2016, 08:32 PM   #5
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Your gut bacteria and fungi definitely change based on your diet and any infections that you might have. Also these bugs will release molecules that will affect you and the other living organisms in you. So, yes, they could make you want to eat more and even more of the "wrong" things.

I believe this can be a reason why people "crave" some foods and also why some diets work for a while, but then your bugs adjust to that diet and you might be back to square one.
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Old 09-28-2016, 08:35 PM   #6
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17 quadrillion flies can't be wrong, eat feces.
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Old 09-28-2016, 09:24 PM   #7
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Coincidentally, I saw the youtube video from sengsational (the OP) making sauerkraut (I think I saw the link when viewing his Orion cooker mod youtube), so I finally got around to making some today. We'll see how it turns out in a few weeks.

I always wanted to, but didn;t really want gallons of it. But I found you can make small batches in mason jars - I used just a half head that we had, plus a carrot, only made about a cup. But it's so easy, I could see making it 2 - 4 cups at a time, and I could try various ingredients (apple, onion, juniper berries, caraway, etc).

So the point is to eat it raw - you get the vitamins and live cultures (mainly lacto-bacillus strains I think). If its good, I'll try to get in the habit of having at least a small amount each day on a sandwich or salad or as a side.

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Old 09-28-2016, 09:43 PM   #8
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We have been making our own kimchee for years, I am always surprised that it hasn't killed us yet.
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Old 09-28-2016, 10:06 PM   #9
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Now you have my interest. I love kimchee and frequent Korean places as well as buy in the grocery. Haven't DIY'ed it yet, but it's on my list.

Links?
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Old 09-28-2016, 11:01 PM   #10
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I was just looking into this a couple of days ago. Haven't done it yet, but it looks easy enough. How to make kimchi in 5 easy steps | MNN - Mother Nature Network
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Old 09-28-2016, 11:31 PM   #11
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Quote:
Originally Posted by sengsational View Post
...
Hmmm. Where did these things come from and how long have they been with "me". Is "me" really "me", or am "I" just a collection of human DNA (yes), plus a bunch of random stuff that is hitch hiking along for the ride?
....
Perhaps the middle ages Royalty had it correct when referring to oneself as "we"
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Old 09-29-2016, 04:43 AM   #12
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Suspect it may be the other way around. Bacteria existed long before we did, and they could consider us to be the interlopers who needed to be dealt with.

Think of all the nonsense we've foisted on them since then: politics, religion, class warfare...wait - maybe all that stuff was THEIR idea! And the obesity thing: they want people to eat more food, so they get more nourishment.

Naturally, they won't like it if we figure out their secret and start actively exerting our wills to defy them. Wait, I'm starting to feel sick. My temperature is rising! If you don't hear from me, you'll know the Gut Biome Overlords have decided to sacrifice me for the greater good...aaaaggghlah#(n32#Y....

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Originally Posted by sengsational View Post
L am "I" just a collection of human DNA (yes), plus a bunch of random stuff that is hitch hiking along for the ride?
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Old 09-29-2016, 07:32 AM   #13
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Its an interesting topic, also wondering is there any definitive proof that probiotics work for individuals that have digestion disorders and are not able to absorb nutrients effectively?
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Old 09-30-2016, 12:37 PM   #14
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There's a study that uses a probiotic called VLS#3 to a positive effect, but I imagine many other strains/brands would also work. But you need a LOT of cfu's...many more than you'd get casually taking the ones from wally world.

Overlord idea, lol, might not be far from the truth. One thing is for sure, once a current set of 'factions' is established, they really don't like to change. The way I look at it, is like the game of thrones...each house (strain of bacteria) found its niche and intends to hold on, by whatever means. Even if the dothraki showed up on the shores of westeros (aka FMT) they probably couldn't manage a take-over. But as we heard, that approach can kill the Bolton's (C-DIFF).

Glad to know the kraut video got someone eating live food! I'm going to do kimchi soon...been meaning to, and now we get weekly organic veggies delivered and sometimes can't eat all of them in the week.
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Old 09-30-2016, 01:24 PM   #15
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Glad to know the kraut video got someone eating live food! I'm going to do kimchi soon...been meaning to, and now we get weekly organic veggies delivered and sometimes can't eat all of them in the week.
Better yet, get out in your own garden. One of our real pleasures of early retirement is that we have plenty of time to spend out in the garden.

Get dirty out there. Lots of soil under your nails. Turn that compost heap. It's alive and you get some healthy sunshine too.
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Old 10-02-2016, 02:40 PM   #16
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Originally Posted by sengsational View Post
...

Glad to know the kraut video got someone eating live food! I'm going to do kimchi soon...been meaning to, and now we get weekly organic veggies delivered and sometimes can't eat all of them in the week.
I took a tiny sample of my mini-batch of home made kraut today (see post #7 - ~ 1 cup in a mason jar).

It's on day 4, most sources talk about 3 to 10 days, or letting it go months in a cool spot. I kept it in a room ~ 67F.

It was very good, very encouraging - I think I'll start another somewhat larger batch while I wait for this one to develop a little further. It's early, at day 4 the cabbage and carrot are still pretty crunchy, it is salty (in a good way), and some definite tangy/tart/vinegary taste. This early though, I'd say it tastes more like a 'refrigerator pickling' process (something we do to serve with Korean food - just let veggies sit in a salt/vinegar and maybe sugar brine for a day or just a few hours in the fridge). So I'll let it go, and I assume it will develop more of a traditional sauerkraut taste and texture.

In small batches like this, it is really, really easy. I spent more time just gathering the right size jar and glass to press it down than anything else. Next batch will take very little time.

Oh, and here's a source for DIY kimchee:



I watched her earlier 'traditional' method, which is mostly the same, but the cabbage is kept together at the base, and there is a LOT of labor in spreading salt on each leaf, rinsing each leaf, again and again, and then spreading paste on each leaf, keeping it all together, then rolling the leaves. In the 'easy' method, the cabbage is just chopped and stirred. Two cups of chili pepper flakes, wow!

But that looks easy to make in small amounts too - I might give it a try - a lot more ingredients though. I love kimchee, but in small amounts. I've added a little of the leftovers to other dishes, and it really can be awesome as a kind of spice - a little added to regular American style coleslaw just takes slaw to a different level, w/o really tasting like kimchee either.

-ERD50
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Old 10-04-2016, 10:25 AM   #17
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Thanks for sharing that video. That's a big bag of chili pepper flakes, wow! And a monster radish too.

For things like this, I do like big batches, but I might need to start out smaller. For kraut, I do 15 lbs because I know I'll eat it eventually, and by the time I'm on my last jar, I've forgotten what a pain it is to make, and get excited about making it again, lol!

As to the taste/consistency, it does get more 'kraut-like' if it goes longer. Never completely like the jarred/canned types (which are actually cooked), but like the health food store live kraut in a bag (or better!) I've had mine fermenting at room temp for months. One thing I do that isn't in the video is to infuse the head space with CO2 (just displaces some oxygen). I have a bike-tire filler with food-grade CO2 and just squirt that through the hole in the bucket lid right before I put on the air lock. Also, not in the video, I spray everything down with Starsan (a no-rinse sanitizer). That way, there's less "gunk" when I open the bucket to transfer the kraut to jars. Not that the gunk will kill me, but it's more appetizing not to have it.

My grandfather and dad described their kraut making process, which was real simple: a grater that fit over the top of a 18 inch diameter crock, shred in the cabbage (right out of the garden...probably just rinsed off the visible mud), threw in some salt, put a hunk of plywood over the top of the crock and held it down with a heavy rock. That's it!

Anyway, on to kimchi (when I get back from vacation), need to add more and varied 'bugs' to my diet! And to mpierce, yes, getting out in the dirt is good too.
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Old 10-04-2016, 10:39 AM   #18
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Yes, I did use starsan on everything - being a brewer I have it on hand, and it's so easy I figured "why not"? It could help keep any surface mold/yeast at bay. The stuff under the surface shouldn't be a problem, the anaerobic lactic bugs will take over.

Didn't think to purge it with CO2 Again, I have it on hand, that would be easy. I also might try the tip of adding a little olive oil to form an O2 barrier - the way my juice glass fits in that mason jar, there is only a small ring of surface exposed, so it would take just a little oil.

Will try all that on my next small batch, probably tomorrow.

And yes, the canned/jarred kraut we buy has been heat treated in the canning process, so no live bugs, and probably some degradation of vitamins as well. I usually heat my kraut when I eat it (on a brat, with a pork chop, etc), so I was wondering if that cooking was destroying all the Vit C (it obviously kills the good bugs), but from what I've read, a short cooking time isn't so bad, maybe a 30% reduction or less. It was the boiling of fresh veggies that was the worst - Vit C leaches out to the water.

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Old 10-08-2016, 09:57 PM   #19
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Is "me" really "me", or am "I" just a collection of human DNA (yes), plus a bunch of random stuff that is hitch hiking along for the ride?
It's not entirely random. You get some bugs from mom in the birth process (less with c-section). Breast milk contains compounds that can only be digested by certain bacteria, so they promote growth of particular strains. Human immune cells actually transport specific bacteria into the breast to go into human milk: https://blogs.scientificamerican.com...n-breast-milk/

The current consensus is that there are 10x as many microbes in/around the body as there are human cells. There may be 100x as much bacterial DNA vs human DNA. Grace Liu has a lot to say about the microbiome: https://thegutinstitute.com
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Old 10-09-2016, 09:53 AM   #20
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Now, that is interesting. I was treated for mastitis (infection of the milk ducts) and when discussing the potential cause, the Dr. informed me that "no bacteria occur naturally in the breast." Meaning, they have to come in from the outside. Usually, from a feeding baby.

[QUOTE=msieweke;1789282]IHuman immune cells actually transport specific bacteria into the breast to go into human milk: [URL="https://blogs.scientificamerican.com/lab-rat/the-bacteria-in-breast-[/QUOTE]
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